This invention relates to high-throughput biomolecule analysis and more particularly to a system that utilizes multifunctional encoded particles.
The ability to quantify multiple proteins, cytokines, or nucleic acid sequences in parallel using a single sample allows researchers and clinicians to obtain high-density information with minimal assay time, sample volume, and cost. Such multiplexed analysis is accompanied by several challenges, including molecular encoding and the need to retain assay sensitivity, specificity, and reproducibility with the use of complex mixtures. There are two broad classes of technologies used for multiplexing: planar arrays (1-3) and suspension (particle-based) arrays (4-21), both of which have application-specific advantages. Numbers in parentheses refer to the references appended hereto, the contents of all of which are incorporated herein by reference. Planar arrays, such as DNA and protein microarrays, are best suited for applications requiring ultra-high-density analysis. In comparison, suspension arrays benefit from solution kinetics, ease of assay modification, higher sample throughput, and better quality control by batch synthesis (22). Although particle-based arrays have been used for high-density genotyping applications (23), they are most favorable over microarrays when detecting a modest number of targets over large populations or when rapid probe-set modification is desired. Whereas planar arrays rely strictly on positional encoding, suspension arrays have used a great number of encoding schemes that can be classified as spectrometric (4-11), graphical (12-16), electronic (17-19), or physical (20, 21).
Spectrometric encoding uses specific wavelengths of light or radiation [including fluorophores (4-7), chromophores (8), photonic structures (9), and Raman tags (10, 11)] to identify a species. Fluorescence-encoded microbeads (4-7) can be rapidly processed by using conventional flow cytometry [or on fiber-optic arrays (24)], making them a popular platform for multiplexing. However, there are several disadvantages of using multiple fluorescent signals as means of barcoding, including (i) the limited barcodes achievable (typically ˜100) because of spectral overlap, (ii) the lack of portability for bulky flow cytometers, (iii) added cost with each fluorescent exciter and detector needed, and (iv) potential interference of encoding fluorescence with analyte-detection fluorescence. For these reasons, single-fluorescence methods exist that use graphical techniques to spatially embed barcodes on microcarriers.
Graphical barcodes rely on the patterning of optical elements on a microcarrier; some examples include striped rods (12, 13), ridged particles (14), and dot-patterned particles (14, 15). The chemistries used to fabricate such particles (metallic or photoresist) require additional coupling chemistries to conjugate biomolecules to the surface, and, in the case of striped rods, each metallic pattern needs to be generated one batch at a time. Typically, the patterns on these particles can only be distinguished if the fluorescence of the target signal is sufficiently high. Another graphical method for microcarrier encoding is the selective photobleaching of codes into fluorescent beads (16). In this method, both particle synthesis and decoding are time-consuming, making it an unlikely candidate for high-throughput analysis. A method that eliminates fluorescence altogether uses radio frequency memory tags (17-19). This approach is very powerful because it allows for nearly unlimited barcodes (>1012) and decouples the barcoding scheme from analyte quantification (fluorescence), but the synthesis of any appreciable number (thousands or millions) of these electronic microchip-based carriers may prove to be expensive and slow. These and several other methods developed for multiplexed analysis have been thoroughly reviewed elsewhere (25, 26).